Wednesday, December 08, 2010

DNA, Phosphorus, and Arsenic

Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.

Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.

Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?

Felisa Wolfe-Simon1 is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,

"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."

Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,

But Jonathan Eisen of UC-Davis doesn't let the scientists off so easily. "If they say they will not address the responses except in journals, that is absurd," he said. "They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature."

My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.

As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.

1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?

16 comments
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Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature?When science is done by press release, the doors have already been opened for full public discussion (such as in the blogs).

Isn't this just another manifestation of the whole 'science is what you do in the lab, and doesn't apply to everyday life' problem? At first we complained about scientists who didn't apply skeptical evidence-based reasoning to their daily lives, now it seems that the divide is being made official.

It's not a rumour that GFAJ-1 is an acronym for "Give Felisa A Job". She says it here:

http://www.abc.net.au/rn/scienceshow/stories/2010/3080342.htm

"Felisa Wolfe-Simon: So I kind of joked, well, I really need a job. And we were tossing around 'Give Felisa a Job', that'll work, GFAJ, 'Give Felisa a Job', and so that's what we're stuck with right now."

I could not agree more. The study was, at best, poorly executed and the claims are not supported by the results. As this study has been so widely reported on in the media, scientists have a moral obligation to comment publicly on it. Contrary to Dr Wolfe-Simon’s assertions, a public debate is not only a ‘proper way to engage in a scientific discourse’, but it is in fact a vital part of good and transparent science. The authors should welcome the opportunity to publicly address the valid criticisms raised by their peers, just as they welcomed the opportunity to publicly present their data to the waiting press.

The paper is a joke but the bigger problem is preposterous claim that no one has a right to say anything about this paper outside the official publication after peer review.

First of all, would that peer review, by any chance, be as obviously ridiculously bad as the one that preceded the paper? And why can she go to the non-peer review channels and her critics cannot?

Bleh. To simplify, the authors have been caught lying for monetary gain, can't admit it now and are trying to come up with excuses. BTW, note this: "Received for publication 1 September 2010. Accepted for publication 8 November 2010." This basically says "accepted without revisions". Glamor mag's zeal to publish sensation strikes again.

I love when she is saying that they don't know the mechanism by which As end up "substituting" P. Because it implies not only that the bugs are promiscuous enough not to see any difference between P04 and AsO4, but ALSO that the bugs have a distinct chemistry for synthesizing DNA. Hmmm.

OMG, it's almost unbearable to hear this Felisa talk about her work in that pompous way. Totally loving her 15 minutes in the limelight, but then refusing to follow up on non-peer reviewed criticism. Good luck getting that job!

The "non-peer reviewed criticism of science is inappropriate" claim is perhaps what gets me the most angry in the whole situation. Livid, actually. It promotes the "private club" aspect of science, as if the researchers and formal reviewers have been smiled upon by the gods of knowledge that the underprivileged lower life forms have been deprived of, and they must now bestow this unquestionable sacred knowledge upon their subjects. Who must bend over and accept in silence.

Yeah, fuck off, science is as full of crooks and idiots as any other field of human activity, and the fact that someone holds credentials doesn't mean all that much at all. Maybe probabilistically, they'd be more likely to spout something that's not pure bullshit, but that does not mean all of us spout non-bullshit, all the time. And open discourse is necessary to keep science transparent and fair, and to negotiate the errors that slip past peer review, which is also full of flaws, by the way. The very idea that all criticisms must be peer reviewed as well is fundamentally scary – the factors that bias the system to accept or reject certain papers and not others will not go away in the criticism round. And glamourmags are full of bias and hidden interests. in other words, censorship.

The whole debacle is quite embarrassing, and I hope it doesn't do too much damage to the image of science in public opinion, which is already shitty enough.

"No administrators or Deans are involved in hiring at any decent research university."

Hahahahaha! OK, I almost laughed my coffee through my nose.

That's like the 'No true Scotsman' fallacy. The fact is, it does happen, even at the 'best' universities, unless we care to define 'best' by something other than research impact, program productivity, or number of faculty with high professional honors.

You make it sound like administrators and Deans are commonly involved in deciding who to hire at major research universities.

I was thinking mostly of hiring at the Assistant Professor level—that the kind of job Felisa is looking for. In my experience that's always handled by departmental search committees. Is your experience different? Which universities?

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.